Afghan troops have regained control of central part of the northeastern city of Kunduz from Taliban fighters after days of intense fighting.

Zafar Hashemi, a deputy spokesman for President Ashraf Ghani, said some "scattered elements of the enemy" remain in Kunduz but that Afghan forces control the main part of the city as operations continue to clear out all Taliban fighters.

He said Ghani had ordered the city, province, and "entire northeastern region" to be cleared of "terrorist groups."

Qamirudin Sediqi, an adviser to the health minister, said medicine and doctors were being flown into the city aboard military planes.

Medical officials and residents said emergency supplies of food had also started arriving to the city, which had a population of some 300,000 before the Taliban captured the city last week.

But reports of dire shortages continue.

Meanwhile, the medical charity Doctors Without Borders (MSF) has demanded that an international investigation be made into U.S. air strikes that destroyed an MSF-run hospital on October 3, killing at least 22 people and injuring dozens of others.

Three separate investigations -- by the U.S. military, NATO, and the Afghan government -- are being conducted on the tragic event that U.S. officials have called a mistake.

But MSF officials called for a fact-finding mission to determine whether the strike violated the Geneva Conventions.

"We cannot rely on an internal military investigation," MSF chief Joanne Liu said on October 7 in Geneva.

Her comments come one day after General John Campbell, the top U.S. and NATO commander in Afghanistan, said the "hospital was mistakenly struck" when Afghan officials called for the raid.

The attack led to all international aid organizations leaving the embattled city amid the continued heavy fighting.

"There are presently no humanitarian agencies left inside Kunduz city," said Jens Laerke, spokesman for the UN humanitarian agency.

"Two UN entities, four national [nongovernmental organizations], and 10 international NGOs have been temporarily relocated due to the ongoing conflict and unstable and fluid security situation in Kunduz."

The exodus of charity groups comes amid renewed attacks by the Taliban, which staged assaults on the police headquarters and other government buildings overnight, only days after the government claimed control over the city.

In Kunduz, Laerke said water and electricity reportedly remained cut-off across much of the city, and most food markets and other shops remained closed.

Laerke said thousands of people have fled Kunduz, and an estimated 8,500 families have been displaced in the northeast as a result of the fighting.

The UN's Laerke said the MSF hospital had been "the only facility of its kind in the entire northeastern region of the country, serving some 300,000 people in Kunduz alone."

Now, he said, "the international aid agencies have been forced out of the city for the time being, so there is essentially no proper health care, no proper trauma care for those left inside the city."

Afghanistan's Public Health Ministry said the destruction of the hospital has jeopardized "vital health, medical, and surgical work of international and local health personnel" working throughout Afghanistan.

"Staff no longer feel safe in any health facility anywhere in the country. And some international health organizations are questioning whether the risks of staying in the country are just too high after such an attack."

Aid agencies are scrambling to gain access to the area so they can assess and address the needs.

Deliveries of food and other basic essentials have not been able to enter Kunduz since the September 28 Taliban assault, said Aslim Sayas, a deputy head of the Afghan disaster management agency.

With the airport closed, he said it was still too dangerous and unpredictable for supplies to be trucked into Kunduz. Instead, he said authorities were helping residents who had fled the city.

"Right now, we are providing food and nonfood items to refugees and displaced people in Takhar, Badakhshan, and Balkh," he said, referring to northern provinces to the east and west of Kunduz.​

The World Health Organization (WHO), meanwhile, announced that it was working with the Health Ministry to get needed medical equipment and supplies into Kunduz and planned to establish a temporary health facility.

It said a medical team of doctors, nurses, anaesthesiologists, and surgeons had arrived at the military hospital in Kunduz on October 5 and were providing services there.

The WHO said it was sending a trauma kit containing drugs and materials to meet the needs of 100 patients requiring surgical care, but that it had been stranded in Puli Kumri due to a roadblock.

"WHO is looking for alternative routes or support from the military to get the kits through to Kunduz regional hospital," it said.